You have run into one of the main negatives with PVA adhesives. It is a form of creep and is a reason that PVA is sort of the king of creep.
Here's something will explain what is happening.
The tendency of the glue to ooze out of joints is one form of creep. A classic example is in a slab edge to edge glueup, such as a table top. When ambient humidity rises the timber and the the glue swell. When the ambient humidity goes down the timber shrinks again, and so does the glue, but the glue doesn't all shrink back into its original place resulting in a line of adhesive disfiguring the finish. Actually, under sustained high humidity my anecdotal observations are that the glue keeps on absorbing moisture and creeps out of the joint without the need for the timber to shrink. The symptoms can also be seen sometimes at the shoulder line of other joints such as mortise and tenons.
Another cause that I've witnessed several times is to make a solid timber slab with edge joints in a fairly humid workshop without climate control using PVA as described before. Then right away get to planing and preparing the surface ready for polishing with scrapers, sanding, etc.. Right after that apply the polish, whether it be varnish, pre-cat, or another finish, and take the piece into a drier house, either heated or air conditioned. Three to five days later the rows of pimples will be apparent as the timber shrinks.
There is little you can do about the raised glue lines except to continue to scrape them down periodically. After a few cycles of seasonal humidity changes, they generally stabilize. I would not apply a film finish like varnish or poly varnish. The glue line raising will continue as noted above and they will raise the finish. An oil/varnish finish is much easier to reapply than having to heavily sand or strip a film finish.
Many professional shops do not use a PVA adhesive for panels. Instead, a urea formaldehyde adhesive like DAP/Weldwood Plastic Resin is used.